LitInspector Help

LitInspector is Genomatix' literature search tool for automatic gene and signal transduction pathway data mining within the complete NCBI's PubMed database containing more than 18 Mio. publications. Software guided gene recognition and color coding increases the readability of abstracts. This way LitInspector can significantly speed up literature searches for the scientist. At the same time the scientist retains full control over the software processed data as the sentences and the complete abstracts remain available.

LitInspector allows input of gene synonyms or gene IDs and free text. At least one gene synonym or free text word or phrase has to be submitted. The query, in addition, can be filtered for only those abstracts for which also defined keyword categories (tissue, disease, pathway, or small molecule) were identified.

Enter a single gene symbol or the full gene name or any
valid gene synonym. Example: WT1 or wt 1 or Wilms tumor 1 will be identified as the gene with gene ID 7490. You can also directly enter the
gene ID like 7490. Case sensitivity is not required. Dashes (-) in
gene names as in WT-1 are not necessary and interpreted as blanks like in WT 1.
Wildcards are allowed (WT* or *WT*). Please note that the entered gene name has to consist of
more than two letters or numbers.

If the entered gene name is ambiguous (e.g. a homonym) an intermediate
page will open where you can select the right gene.

You have the possibility to enter up to three different genes. The
genes can be combined with AND or OR (please use capital letters; default is AND).

Enter a search term like liver or a phrase like liver disease.
Different search terms can be combined using the boolean operators OR/AND.
Example: liver OR hepatic AND disease. Please do not type wildcards, parentheses, or quotation marks.

Check for presence of keyword categories assigned to MeSH Terms.
Available categories are tissue and disease.

Filter for classifiers in the abstract

Check for presence of keyword categories occurring in the
abstract. Available categories are tissue, disease, pathway, and small molecule.
Please note: in case of
free text searches, only sentences containing a keyword from the
selected category are shown.

Highlight in the output

Define which keywords will be highlighted in the output. Per
default, transcription factors and genes are highlighted.
The following keyword categories are available:

TF (Transcription Factor)

Gene

Tissue

Disease

Pathway

Function (a "Function" word is a term that can be used to
describe the function of a gene)

Note: If a filter for classifiers in the abstract (Tissue, Disease,
Pathway, or Small molecule) is selected, the corresponding highlighting is automatically
enabled. Please also note that this feature is only available when
LitInspector is started from the Genomatix Suite main menu.

Gene search

Usually, a single gene synonym is entered in the LitInspector form. An advantage of a LitInspector search is, that the submission of a single synonym will automatically consider all synonyms of this gene. For instance, each of the more than 28,000 human genes in the database has six or seven synonyms on average. Entering one gene synonym like "CARD4" (caspase recruitment domain 4) will automatically consider all synonyms of this gene, for instance "NOD1" (nucleotide-binding oligomerization domain containing 1). In the same way entering the gene-ID "10392" will consider the synonyms "CARD4" as well as "NOD1". Note: the user keeps the possibility to search only for a special synonym by combining a gene search with a full text search.

If the entered gene synonym is unique (example: WT1), LitInspector directly opens a page with the Query Info and the Results. The Results are all sentences of the abstract in which the query gene was identified. A maximum of 100 abstracts is shown on one results page, in case of further matches these are available using the "Next Page" button.

If the entered synonym is a homonym, i.e. one and the same synonym is used for two or more different genes (example: MBP), an intermediate page will open and the user can select the demanded gene(s).

Example:

If the entered synonym cannot be found in the database, LitInspector will automatically perform a wildcard search, adding the wildcard at the end of the entered gene name (example: PAX -> PAX*). If still no gene can be assigned to the entered synonym, the best way is to try the gene ID directly.

It is also possible to scan for two or three different genes. Please use the separate form fields for each single gene. In this case an intermediate page will open; please select the relevant genes using the checkboxes and choose the radio button for boolean OR or AND combination of the different query genes.

Example:

Enter "WT1" in the first form field and "PAX" in the second form field. In the intermediate page you can select "WT1" as gene number one and "PAX2" as gene number two. If you choose the radio button "AND connection between different selected genes" (default), the LitInspector result will show only papers where WT1 and PAX2 are tagged in the same abstract.

Free text search

Free text searches are also possible with LitInspector. A single word or a phrase can be entered. Different search terms can be combined using boolean OR or AND. Please do not type wildcards, parentheses, or quotation marks. Free text searches may take some minutes, especially searches for abundant words like e.g. "cancer" or "blood".

Gene searches and free text searches can be combined. Example: "WT1" is entered in the gene form field together with "kidney development OR renal development" in the free text field. The result will show all abstract sentences where the gene WT1 was tagged and the phrase ("kidney development" OR "renal development") was found in the same abstract.

Please note that in contrast to genes or keywords free text search terms do not necessarily occur in the selection of sentences shown in the LitInspector results page. The reason for that is, that only sentences containing also tagged genes or keywords are shown in the results. If the free text search phrase is in a sentence that does not contain a tagged word, the sentence is not shown in the output. However, it is contained in the abstract which can be proven by following the NCBI PubMed link. If the free text search phrase is contained in a sentence displayed in the LitInspector results the free text terms are underlined.

The checkbox under the free text search supplies a powerfull tool to analyze associations of the entered search terms with LitInspector classifiers, i.e. genes, transcription factors, diseases, tissues, small molecules, and pathways. Entering your search terms within the free text search and additionally selecting the check box beneath will start the analysis. Calculation takes several minutes.

The result page lists terms from the different key word categories co-cited with the user defined search terms. Significance criteria are co-citation in at least four PubMed abstracts and a two fold overrepresentation compared to the background of all PubMed abstracts. This focuses to the most relevant associations and impedes random results dominated by abundant key words like 'p53' or 'neoplasms'. The results can be downloaded as tab delimited files.

Additional filters

LitInspector supplies additional filters that facilitate the identification of abstracts containing certain keyword categories like Tissue, Disease , Pathway, or Small molecule. These filters are working only together with a gene or free text search. Example: entering "WT1" and additionally checking the keyword category "Pathway" will restrict the LitInspector results to only those abstracts that contain the gene Wt1 together with pathway keywords like "signal transduction" or "signaling". This filtering is intended to pre-select papers that may deal with signal transductions involving WT1. In the same way a search for "WT1" and a filtering for the keyword category "Disease" should pre-select papers dealing with diseases where WT1 could be involved. The "Tissue" filter could be used for identification of the tissue specificity of a gene.

Query Info

Output example:

The Query Info summarizes the input parameters.
In case of a gene search the query info gives further information
about the selected gene, directly or in form of links.
The official gene synonym and gene name is shown as well as the gene ID with a link to search the Genomatix databases for that gene.
If the gene is known as transcription factor, this information is given
and also a link to its DNA-binding site definition (Genomatix' matrix family) if available.
The number of citations is the total number of PubMed abstracts wherein the
gene is identified.

Search Results

Output example:

The LitInspector search results are PubMed abstracts where genes and relevant keywords are highlighted.
The color code of the highlighted words is explained above the results.
The journal title and the year of publication are shown for each of the found abstracts
as well as the PubMed-ID, providing a link to the original abstract at the NCBI.
The abstract is splitted in single sentences, the information of the sentence number is given
at the left side (TI = title, AB = abstract).
In case of a gene search all sentences containing a synonym of this gene are displayed.
Each highlighted gene or transcription factor links to the "Search Genomatix databases" for more gene info. In case of a full text search all sentences of a matching PubMed abstract are displayed
that contain at least one tagged word or phrase.

Statistics

Output example:

The statistics shows how many PubMed abstracts were scanned in the
current analysis (absolute and in percent from complete PubMed). In addition,
the total number of PubMed abstracts in the database is given as well as the the number
of abstracts found so far.
Each LitInspector
output page contains a maximum of 100 abstracts. If further matches are available,
they can be retrieved by pressing the "Next Page" button.
In case the complete PubMed has been scanned, this information is displayed at the bottom of the statistics.

The "Get Selected Abstracts" button generates a link to all
publications manually selected using the check boxes in front of the journal titles
in the LitInspector result page.
You can choose between the LitInspector format with the color coded sentences or a direct link to the NCBI PubMed abstracts.

Genomatix Signal Transduction Pathways are obtained by literature
data mining based on all available PubMed abstracts.
The output table lists the pathway associations identified for the entered gene
ordered by the number of references (column "Ref."), i.e. PubMed abstracts. By clicking
the number you get access to the references as color coded sentences in LitInspector format (the link is limited to
the newest 100 abstracts). The Pathway Component specifies the signaling element
that was identified to be associated with your entered gene. The pathway components themselves are assigned to Signaling Pathways.
Signaling pathway associations that are statistically overrepresented
for this gene compared to the background of all gene to pathway
associations are marked with an asterisk
(overrepresentation more than two fold and p-value less than 0.05).
To get an overview, most pathways are referenced by a graphical representation, referring to BioCarta, STKE, or KEGG.